We couldn't find specific rules, so we decided it was a called shot (-4)

We hit with a raise and someone said that there was no extra damage die because it was an object

we rolled damage (exploding)

we couldn't decide which was the correct toughness for a tire, and finally settled for a 9

we kept playing and having fun (golden rule ) but we feel we didn't handle it good.

Which are the correct rules for shooting tires?

There isn't a specific rule for that in the core rules other than perhaps what your group did, used a Called Shot and set the Toughness based on the examples given (though personally 9 might be a bit high for a tire).

I would note that vehicles are not subject to the rules for Breaking Things. As noted in that section, " Use these rules for solid objects. Larger objects with many components (such as vehicles) take multiple hits as per the vehicle rules." So damage can Ace and a raise does provide an extra die of damage when attacking a vehicle.